'\" t .\" Title: gt-repfind .\" Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author] .\" Generator: DocBook XSL Stylesheets vsnapshot .\" Date: 07/22/2020 .\" Manual: GenomeTools Manual .\" Source: GenomeTools 1.6.1 .\" Language: English .\" .TH "GT\-REPFIND" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" gt-repfind \- Compute maximal exact matches (and more)\&. .SH "SYNOPSIS" .sp \fBgt repfind\fR [options] \-ii indexname .SH "DESCRIPTION" .PP \fB\-l\fR [\fIvalue\fR] .RS 4 Specify minimum length of matches (default: 0) .RE .PP \fB\-f\fR [\fIyes|no\fR] .RS 4 Compute forward matches (default: yes) .RE .PP \fB\-r\fR [\fIyes|no\fR] .RS 4 Compute reverse matches (default: no) .RE .PP \fB\-p\fR [\fIyes|no\fR] .RS 4 Compute matches on reverse strand (default: no) .RE .PP \fB\-seedlength\fR [\fIvalue\fR] .RS 4 Specify minimum length of seed (default: 0) .RE .PP \fB\-maxfreq\fR [\fIvalue\fR] .RS 4 Specify maximal frequency of maximal exact matches in reference sequence (default: 0) .RE .PP \fB\-extendxdrop\fR [\fIvalue\fR] .RS 4 Extend seed to both sides using xdrop algorithm, optional parameter specifies sensitivity (default: 97) .RE .PP \fB\-xdropbelow\fR [\fIvalue\fR] .RS 4 Specify xdrop cutoff score (argument 0 means undefined)\&. If undefined an optimal value is determined automatically depending on the error rate .RE .PP \fB\-extendgreedy\fR [\fIvalue\fR] .RS 4 Extend seed to both sides using greedy algorithm with trimming of waves, optional parameter specifies sensitivity (default: 97) .RE .PP \fB\-minidentity\fR [\fIvalue\fR] .RS 4 Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop and greedy extension) (default: 80) .RE .PP \fB\-ii\fR [\fIstring\fR] .RS 4 Specify input index (default: undefined) .RE .PP \fB\-outfmt\fR .RS 4 specify what information about the matches to display alignment: show alignment (possibly followed by = to specify width of alignment columns, default is ) seed_in_algn: mark the seed in alignment polinfo: add polishing information for shown alignment seed: abbreviation for seed\&.len seed\&.s seed\&.q failed_seed: show the coordinates of a seed extension, which does not satisfy the filter conditions fstperquery: output only the first found match per query tabsep: separate columns by tabulator, instead of space as default blast: output matches in blast format 7 (tabular with comment lines; instead of gap opens, indels are displayed) gfa2: output matches in gfa2 format custom: output matches in custom format, i\&.e\&. no columns are pre\-defined; all columns have to be specified by the user cigar: display cigar string representing alignment (no distinction between match and mismatch) cigarX: display cigar string representing alignment (distinction between match (=) and mismatch (X)) trace: display trace, i\&.e\&. a compact representation of an alignment (possibly followed by =) to specify the delta\-value; default value of delta is 50 dtrace: display trace as differences; like trace, but instead of an absolute value x, report the difference delta\-x\&. This leads to smaller numbers and thus a more compact representation s\&.len: display length of match on subject sequence s\&.seqnum: display sequence number of subject sequence subject id: display sequence description of subject sequence s\&.start: display start position of match on subject sequence s\&.end: display end position of match on subject sequence strand: display strand of match using symbols F (forward) and P (reverse complement) q\&.len: display length of match on query sequence q\&.seqnum: display sequence number of query sequence query id: display sequence description of query sequence q\&.start: display start position of match on query sequence q\&.end: display end position of match on query sequence alignment length: display length of alignment mismatches: display number of mismatches in alignment indels: display number of indels in alignment gap opens: display number of indels in alignment score: display score of match editdist: display unit edit distance identity: display percent identity of match seed\&.len: display length seed of the match seed\&.s: display start position of seed in subject seed\&.q: display start position of seed in query s\&.seqlen: display length of subject sequence in which match occurs q\&.seqlen: display length of query sequence in which match occurs evalue: display evalue bit score: display bit score .RE .PP \fB\-evalue\fR [\fIvalue\fR] .RS 4 switch on evalue filtering of matches (optional argument specifies evalue threshold) (default: 10\&.000000) .RE .PP \fB\-scan\fR [\fIyes|no\fR] .RS 4 scan index rather than map it to main memory (default: no) .RE .PP \fB\-v\fR [\fIyes|no\fR] .RS 4 be verbose (default: no) .RE .PP \fB\-help\fR .RS 4 display help and exit .RE .PP \fB\-version\fR .RS 4 display version information and exit .RE .SH "REPORTING BUGS" .sp Report bugs to \&.